Phred argument in Staden

Malcolm Cook mec at stowers-institute.org
Thu May 15 03:12:53 EST 2003


Pinar,

I'm confused by your statement of the problem.

You say you are using pregap4, but your examples look like you are calling
phred from the UNIX command line, rather than filling in the argument window
for the Phred module in pregap4.

In any case, the -cd option does not make sense to use when using phred with
pregap4, since the pregap4 phred module writes SCF formatted versions of
each trace file in the current directory, and rewrites the experiment files
to refer to this file, again IN THE WORKING DIRECTORY.

What are you trying to accomplish?  Perhaps you do not need pregap4 for your
purposes..

Malcolm



"Pinar Kondu" <pkondu at attbi.com> wrote in message
news:Vscwa.575385$OV.547171 at rwcrnsc54...
> Hi everyone,
>
> I am trying to configure Phred in Pregap4. In the argument window for
Phred
> module I am putting the following. Program gives me the error message
> "use -cd with more than one input file".
> Since I am using it, it seems not to be recognizing my argument. I also
> tried putting double quotes around, didn't help. Any advice?
>
> /usr/local/share/biotools/Phred/phred
> /var/www/html/seqanal/runphred/abifiles/*.abi
> -cd  /usr/local/share/seqfiles/processed/phredded
>
> (I also tried as:
> /usr/local/share/biotools/Phred/phred
> /var/www/html/seqanal/runphred/abifiles
> -cd  /usr/local/share/seqfiles/processed/phredded
>
> AND
>
> /usr/local/share/biotools/Phred/phred  .*abi
> -cd  /usr/local/share/seqfiles/processed/phredded
> )
>
>
> note:
> Phred location:
>  /usr/local/share/biotools/Phred/phred
>
> Location of the .abi files that I am adding in the "Files to Process of
> Pregap4":
> /var/www/html/seqanal/runphred/abifiles/
>
> I am defining a directory for the output so that I can use the "-cd"
option:
> /usr/local/share/seqfiles/processed/phredded
>
>
>
> many thanks,
> Pinar
>
>
>
>




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